Analysis of the algorithm: From embeddings to prioritized genes.

The algorithm transformed the similarity matrix to make it compatible with the embedding process. Once this was done for each network and embedding type, it was integrated by embedding type. Below there is a general analysis of the properties of each matrix in the different phases of the process, including the graph building process for each layer.

Annotations Properties

Table 1. Annotation descriptors.

Net Min Max Average Standard_Deviation
DepMap_effect 972 17354 2043.6562906724512 3829.1218209282715
biological_process 1 1028 8.120165122974988 20.640289926561053
cellular_component 1 5172 7.219656420451649 82.56741928666138
disease 1 560 3.020024353943986 10.754332485855503
gene_PS 1 108 2.1519058295964126 5.045578888786698
gene_TF 1 5778 3.0320060963993143 74.46796191948712
gene_hgncGroup 1 2203 2.2641919701793896 22.399942274692194
hippie_ppi 1 2576 45.37051659901017 93.00135289510746
molecular_function 1 6791 4.87167748867193 54.08093332133869
pathway 1 479 6.75436035343834 16.179001796162975
phenotype 1 1230 24.12071988924781 49.500241778889524
string_ppi_coexpression 1 3569 317.42410862126064 343.22065801422775
string_ppi_combined_score 1 7483 602.2932856446106 518.3682018941319
string_ppi_cooccurence 1 133 20.415675297410775 27.990489848424655
string_ppi_database 1 1287 64.01997573042098 86.01865153961889
string_ppi_exp 1 4192 249.92115027829314 354.50679835712316
string_ppi_experimental 1 4192 249.92115027829314 354.50679835712316
string_ppi_fusion 1 101 3.721608040201005 7.370788836174388
string_ppi_neighborhood 1 1391 92.45592392701106 127.04630294501078
string_ppi_textmining 1 7472 496.94524714828896 457.77184250900143

Individual Processing Graph steps

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Embedding Process

Table 2. Uncombined Embedding Matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
DepMap_effect_pearson ct 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson el 17354x17354 301161316 301161316 1.0
DepMap_effect_pearson ka 17354x17354 301161316 106778670 0.35455639329189276
DepMap_effect_pearson node2vec 17354x17354 301161316 301161314 0.9999999933590409
DepMap_effect_pearson rf 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ct 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman el 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman ka 17354x17354 301161316 194719108 0.6465608219084817
DepMap_effect_spearman node2vec 17354x17354 301161316 301161316 1.0
DepMap_effect_spearman rf 17354x17354 301161316 301161316 1.0
biological_process ct 16972x16972 288048784 288048784 1.0
biological_process el 16972x16972 288048784 288048784 1.0
biological_process ka 16972x16972 288048784 246522392 0.8558355587434107
biological_process node2vec 16972x16972 288048784 288048784 1.0
biological_process raw_sim 16972x16972 288048784 246522392 0.8558355587434107
biological_process rf 16972x16972 288048784 288048784 1.0
cellular_component ct 17963x17963 322669369 322669369 1.0
cellular_component el 17963x17963 322669369 322669369 1.0
cellular_component ka 17963x17963 322669369 322669369 1.0
cellular_component node2vec 17963x17963 322669369 322669369 1.0
cellular_component rf 17963x17963 322669369 322669369 1.0
disease ct 7618x7618 58033924 58033924 1.0
disease el 7618x7618 58033924 58033924 1.0
disease ka 7618x7618 58033924 54856102 0.9452419932865473
disease node2vec 7618x7618 58033924 58033924 1.0
disease raw_sim 7618x7618 58033924 54856102 0.9452419932865473
disease rf 7618x7618 58033924 58033924 1.0
gene_PS ct 3020x3020 9120400 8927292 0.978826805841849
gene_PS el 3020x3020 9120400 5842664 0.6406148853120477
gene_PS ka 3020x3020 9120400 98718 0.010823867374237971
gene_PS node2vec 3020x3020 9120400 9120400 1.0
gene_PS rf 3020x3020 9120400 5842664 0.6406148853120477
gene_TF ct 3871x3871 14984641 14984637 0.9999997330600046
gene_TF el 3871x3871 14984641 14969165 0.9989672091576969
gene_TF ka 3871x3871 14984641 5275373 0.35205201112258877
gene_TF node2vec 3871x3871 14984641 14984641 1.0
gene_TF rf 3871x3871 14984641 14969165 0.9989672091576969
gene_hgncGroup ct 24296x24296 590295616 589800760 0.9991616810516851
gene_hgncGroup el 24296x24296 590295616 310647638 0.5262577420192123
gene_hgncGroup ka 24296x24296 590295616 12955070 0.021946749474080457
gene_hgncGroup node2vec 24296x24296 590295616 590295616 1.0
gene_hgncGroup raw_sim 24296x24296 590295616 12930774 0.021905590435555598
gene_hgncGroup rf 24296x24296 590295616 310647638 0.5262577420192123
hippie_ppi ct 13444x13444 180741136 180714249 0.9998512402843368
hippie_ppi el 13444x13444 180741136 175403916 0.9704703637582537
hippie_ppi ka 13444x13444 180741136 213164 0.0011793884044194567
hippie_ppi node2vec 15763x15763 248472169 248472167 0.9999999919508088
hippie_ppi rf 13444x13444 180741136 175403916 0.9704703637582537
molecular_function ct 17333x17333 300432889 300432889 1.0
molecular_function el 17333x17333 300432889 300432889 1.0
molecular_function ka 17333x17333 300432889 300432889 1.0
molecular_function node2vec 17333x17333 300432889 300432889 1.0
molecular_function rf 17333x17333 300432889 300432889 1.0
pathway ct 5611x5611 31483321 31482925 0.9999874219114305
pathway el 5611x5611 31483321 25851467 0.8211162666098663
pathway ka 5611x5611 31483321 362997 0.011529819233491919
pathway node2vec 5611x5611 31483321 31483321 1.0
pathway rf 5611x5611 31483321 25851467 0.8211162666098663
phenotype ct 3806x3806 14485636 14485636 1.0
phenotype el 3806x3806 14485636 14485636 1.0
phenotype ka 3806x3806 14485636 14485636 1.0
phenotype node2vec 3806x3806 14485636 14485636 1.0
phenotype raw_sim 3806x3806 14485636 14485636 1.0
phenotype rf 3806x3806 14485636 14485636 1.0
string_ppi_coexpression ct 18118x18118 328261924 328261924 1.0
string_ppi_coexpression el 18118x18118 328261924 327682444 0.9982347023592051
string_ppi_coexpression ka 18118x18118 328261924 5769202 0.017574995996185047
string_ppi_coexpression node2vec 18118x18118 328261924 328261924 1.0
string_ppi_coexpression raw_sim 18118x18118 328261924 5751087 0.017519811405236264
string_ppi_coexpression rf 18118x18118 328261924 327682444 0.9982347023592051
string_ppi_cooccurence ct 2858x2858 8168164 8167760 0.9999505396806431
string_ppi_cooccurence el 2858x2858 8168164 1409490 0.17255897408524118
string_ppi_cooccurence ka 2858x2858 8168164 61198 0.007492258970314504
string_ppi_cooccurence node2vec 2858x2858 8168164 8168164 1.0
string_ppi_cooccurence raw_sim 2858x2858 8168164 58344 0.007142853644956198
string_ppi_cooccurence rf 2858x2858 8168164 1409490 0.17255897408524118
string_ppi ct 18453x18453 340513209 340513209 1.0
string_ppi_database ct 10713x10713 114768369 114768099 0.9999976474354184
string_ppi_database el 10713x10713 114768369 109307927 0.9524220650029452
string_ppi_database ka 10713x10713 114768369 696547 0.006069154820872291
string_ppi_database node2vec 10713x10713 114768369 114768369 1.0
string_ppi_database raw_sim 10713x10713 114768369 685840 0.005975862565407722
string_ppi_database rf 10713x10713 114768369 109307927 0.9524220650029452
string_ppi el 18453x18453 340513209 340513209 1.0
string_ppi_exp ct 17248x17248 297493504 297493504 1.0
string_ppi_exp el 17248x17248 297493504 297183146 0.9989567570524162
string_ppi_exp ka 17248x17248 297493504 4327866 0.014547766394253772
string_ppi_exp node2vec 17248x17248 297493504 297493504 1.0
string_ppi_exp rf 17248x17248 297493504 297183146 0.9989567570524162
string_ppi_experimental ct 17248x17248 297493504 297493504 1.0
string_ppi_experimental el 17248x17248 297493504 297183146 0.9989567570524162
string_ppi_experimental ka 17248x17248 297493504 4327866 0.014547766394253772
string_ppi_experimental node2vec 17248x17248 297493504 297493504 1.0
string_ppi_experimental raw_sim 17248x17248 297493504 4310629 0.014489825633301895
string_ppi_experimental rf 17248x17248 297493504 297183146 0.9989567570524162
string_ppi_fusion ct 5970x5970 35640900 35639688 0.9999659941247275
string_ppi_fusion el 5970x5970 35640900 15344240 0.43052335939889286
string_ppi_fusion ka 5970x5970 35640900 28186 0.0007908330036559122
string_ppi_fusion node2vec 5970x5970 35640900 35640900 1.0
string_ppi_fusion raw_sim 5970x5970 35640900 22217 0.0006233568737040872
string_ppi_fusion rf 5970x5970 35640900 15344240 0.43052335939889286
string_ppi ka 18453x18453 340513209 11132537 0.03269340720347797
string_ppi_neighborhood ct 3891x3891 15139881 15139881 1.0
string_ppi_neighborhood el 3891x3891 15139881 15139881 1.0
string_ppi_neighborhood ka 3891x3891 15139881 363637 0.024018484689542804
string_ppi_neighborhood node2vec 3891x3891 15139881 15139881 1.0
string_ppi_neighborhood raw_sim 3891x3891 15139881 359746 0.02376148134849937
string_ppi_neighborhood rf 3891x3891 15139881 15139881 1.0
string_ppi node2vec 18453x18453 340513209 340513209 1.0
string_ppi raw_sim 18453x18453 340513209 11114101 0.03263926539777786
string_ppi rf 18453x18453 340513209 340513209 1.0
string_ppi_textmining ct 18410x18410 338928100 338928100 1.0
string_ppi_textmining el 18410x18410 338928100 338928100 1.0
string_ppi_textmining ka 18410x18410 338928100 9167158 0.02704750063509045
string_ppi_textmining node2vec 18410x18410 338928100 338928100 1.0
string_ppi_textmining raw_sim 18410x18410 338928100 9148755 0.02699320298316959
string_ppi_textmining rf 18410x18410 338928100 338928100 1.0

Table 3. Integrated Embedding Matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero Matrix_Non_Zero_Density
geometric_mean ct 29448x29448 867184704 761938554 0.8786346789622341
geometric_mean el 29448x29448 867184704 482062204 0.5558933428788891
geometric_mean ka 29448x29448 867184704 27007336 0.03114369508067338
geometric_mean node2vec 29448x29448 867184704 762143880 0.8788714520499661
geometric_mean raw_sim 29448x29448 867184704 26978260 0.031110165891486942
geometric_mean rf 29448x29448 867184704 482062204 0.5558933428788891
integration_mean_by_presence ct 29448x29448 867184704 761944566 0.8786416117413436
integration_mean_by_presence el 29448x29448 867184704 563575710 0.6498912024167807
integration_mean_by_presence ka 29448x29448 867184704 270353858 0.3117604090027861
integration_mean_by_presence node2vec 29448x29448 867184704 762143880 0.8788714520499661
integration_mean_by_presence raw_sim 29448x29448 867184704 270342016 0.3117467533191176
integration_mean_by_presence rf 29448x29448 867184704 563575710 0.6498912024167807
max ct 29448x29448 867184704 761748110 0.878415067155059
max el 29448x29448 867184704 563575710 0.6498912024167807
max ka 29448x29448 867184704 270353858 0.3117604090027861
max node2vec 29448x29448 867184704 762143880 0.8788714520499661
max raw_sim 29448x29448 867184704 270342016 0.3117467533191176
max rf 29448x29448 867184704 563575710 0.6498912024167807
mean ct 29448x29448 867184704 761944566 0.8786416117413436
mean el 29448x29448 867184704 563575710 0.6498912024167807
mean ka 29448x29448 867184704 270353858 0.3117604090027861
mean node2vec 29448x29448 867184704 762143880 0.8788714520499661
mean raw_sim 29448x29448 867184704 270342016 0.3117467533191176
mean rf 29448x29448 867184704 563575710 0.6498912024167807
median ct 29448x29448 867184704 761934052 0.87862948745
median el 29448x29448 867184704 563464204 0.6497626185067028
median ka 29448x29448 867184704 77718728 0.08962188521258788
median node2vec 29448x29448 867184704 762143880 0.8788714520499661
median raw_sim 29448x29448 867184704 77695049 0.0895945796110352
median rf 29448x29448 867184704 563464204 0.6497626185067028

Weight values